private static double[,] getRegularBins(double _firstMz, double _lastMz, quadraticEquation _par)
{
ArrayList regularBinsArrayList = new ArrayList();
double x = _firstMz;
while (x <= _lastMz)
{
regularBinsArrayList.Add(x);
x += _par.A + _par.B * (x - _par.x0) + _par.C * Math.Pow(x - _par.x0, 2);
}
double[,] regularBins = new double[2, regularBinsArrayList.Count];
for (int i = 0; i < regularBinsArrayList.Count; i++)
{
regularBins[0, i] = (double)regularBinsArrayList[i];
}
return(regularBins);
}
private static quadraticEquation getBinParameters(double[,] firstSpectrum)
{
quadraticEquation par = new quadraticEquation();
par.x0 = firstSpectrum[0, 0];
int totElements = ((double[, ])firstSpectrum).GetUpperBound(1) + 1;
double[] mzs = new double[totElements];
for (int i = 0; i < totElements; i++)
{
mzs[i] = firstSpectrum[0, i];
}
double[] distances = new double[totElements];
for (int i = 0; i < totElements - 1; i++)
{
distances[i] = mzs[i + 1] - mzs[i];
}
// get local median
int localSize = 200; // this must be an even number
double[,] medianDistances = new double[2, totElements - localSize];
for (int i = localSize / 2 + 1; i < totElements - (localSize / 2 - 1); i++)
{
double[] localDistances = new double[localSize];
for (int j = 0; j < localSize; j++)
{
localDistances[j] = distances[j + (i - localSize / 2 - 1)];
}
// bubble sort
for (int k = localSize; k >= 0; k--)
{
for (int l = localSize - 1; l > 0; l--)
{
if (localDistances[l] < localDistances[l - 1])
{
double prov = localDistances[l - 1];
localDistances[l - 1] = localDistances[l];
localDistances[l] = prov;
}
}
}
// get median
medianDistances[0, i - (localSize / 2 + 1)] = firstSpectrum[0, i];
medianDistances[1, i - (localSize / 2 + 1)] = (localDistances[localSize / 2 - 2]
+ localDistances[localSize / 2 - 1]) / 2;
}
Smoother smoothy = new Smoother();
smoothy.original = medianDistances;
double[] coeffs = smoothy.quadraticCoefficientsABC;
par.A = coeffs[0];
par.B = coeffs[1];
par.C = coeffs[2];
par.initialValue = smoothy.initialValue;
par.hasBeenCalculated = true;
return(par);
}
public double[,] getAveragedSpectrum(int _peakStart,
int _peakEnd,
int _peakMax,
bool _takeInflections, // must be an odd number
int _totSpectraTaken, // 0 means all of them
double _firstMz,
double _lastMz,
int _maxNumberOfZeros,
ref quadraticEquation _par,
Label _status)
{
ArrayList spectra = new ArrayList();
if (_totSpectraTaken == 0) // 0 means all of them
{
spectra = takeAllFullsInRange(_peakStart, _peakEnd);
}
else
{
double RTstart = getRTfromScanNumber(_peakStart);
double RTmax = getRTfromScanNumber(_peakMax);
double RTend = getRTfromScanNumber(_peakEnd);
int totSpectraWithoutInflections = _totSpectraTaken;
if (_takeInflections)
{
totSpectraWithoutInflections -= 2;
}
int lateralTot = (totSpectraWithoutInflections - 1) / 2;
int lastSN = 0; // to avoid duplications
// add left inflection if needed
if (_takeInflections)
{
spectra.Add(getSpectrum(_peakStart));
lastSN = _peakStart;
}
// add scans before the maximum
double RTLateralSize = RTmax - RTstart;
for (int j = lateralTot; j >= 1; j--)
{
double RTnew = RTmax - RTLateralSize * ((double)j / ((double)lateralTot + 1));
int SNnew = getScanNumberOfPrevOrNextSpectrumByType(RTnew,
spectrumPosition.sameOrPrevious, spectrumTypes.Full);
if (lastSN != SNnew)
{
spectra.Add(getSpectrum(SNnew));
lastSN = SNnew;
}
}
// add maximum
if (lastSN != _peakMax)
{
spectra.Add(getSpectrum(_peakMax));
lastSN = _peakMax;
}
// add scans after the maximum
RTLateralSize = RTend - RTmax;
for (int j = 1; j <= lateralTot; j++)
{
double RTnew = RTmax + RTLateralSize * ((double)j / ((double)lateralTot + 1));
int SNnew = getScanNumberOfPrevOrNextSpectrumByType(RTnew,
spectrumPosition.sameOrNext, spectrumTypes.Full);
if (lastSN != SNnew)
{
spectra.Add(getSpectrum(SNnew));
lastSN = SNnew;
}
}
// add right inflection if needed
if (_takeInflections && lastSN != _peakEnd)
{
spectra.Add(getSpectrum(_peakEnd));
}
//if (_totSpectraTaken == 3 && _takeInflections)
//{
// spectra.Add(getSpectrum(_peakStart));
// spectra.Add(getSpectrum(_peakMax));
// spectra.Add(getSpectrum(_peakEnd));
//}
}
double[,] regularBins = new double[0, 0];
if (spectra == null)
{
return(null);
}
double[,] firstSpectrum = (double[, ])spectra[0];
//double[,] secondSpectrum = (double[,])spectra[1];
//double[,] thirdSpectrum = (double[,])spectra[2];
if (!_par.hasBeenCalculated)
{
_status.Text = "Calculating bin size parameters...";
Application.DoEvents();
string rawFile = _par.rawFilePath;
_par = getBinParameters(firstSpectrum);
_par.rawFilePath = rawFile;
}
if (regularBins.Length == 0)
{
regularBins = getRegularBins(_firstMz, _lastMz, _par);
}
int allowedMargin = 4;
ArrayList spectraNewBins = getSpectraInNewBins(regularBins, spectra, allowedMargin);
double[,] spectrumAverage = calculateAveragedSpectrum(spectraNewBins, allowedMargin);
//saveIndividualSpectrum(firstSpectrum, "x1");
//saveIndividualSpectrum(secondSpectrum, "x2");
//saveIndividualSpectrum(thirdSpectrum, "x3");
//saveIndividualSpectrum(spectrumAverage, "xaverage");
return(spectrumAverage);
}
